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Human TRIM21 PRYSPRY domain in complex with AL236
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IWG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3.5 298 2.3 M Sodium Chloride
0.1 M Sodium Citrate
Crystal Properties Matthews coefficient Solvent content 2.32 46.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.75 α = 90 b = 67.75 β = 90 c = 71.114 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 X 16M 2025-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.45 58.67 100 0.079 0.081 0.018 0.999 19.5 20.7 32898
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.47 100 1.516 1.557 0.349 0.819 19.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.45 58.67 31293 1571 99.97 0.15102 0.15044 0.1646 0.162 0.1756 RANDOM 20.862
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.39 -0.2 -0.39 1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.217 r_long_range_B_refined 10.809 r_long_range_B_other 10.611 r_dihedral_angle_1_deg 7.39 r_scangle_other 6.336 r_mcangle_other 6.21 r_mcangle_it 6.207 r_dihedral_angle_2_deg 5.237 r_scbond_it 4.173 r_scbond_other 4.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.217 r_long_range_B_refined 10.809 r_long_range_B_other 10.611 r_dihedral_angle_1_deg 7.39 r_scangle_other 6.336 r_mcangle_other 6.21 r_mcangle_it 6.207 r_dihedral_angle_2_deg 5.237 r_scbond_it 4.173 r_scbond_other 4.17 r_mcbond_it 4.016 r_mcbond_other 3.974 r_rigid_bond_restr 1.924 r_angle_refined_deg 1.356 r_angle_other_deg 0.491 r_chiral_restr 0.071 r_gen_planes_refined 0.006 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1418 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction MOLREP phasing